We report our experience of electrical stimulation and biofeedback exercise of pelvic floor muscle for children with faecal incontinence after surgery for anorectal malformation (ARM). Electrical stimulation and biofeedback exercise of pelvic floor muscle were performed on children with post-operative faecal soiling following repair of intermediate or high type ARM. Children under the age of 5 years or with learning difficulties were excluded. They had 6 months supervised programme in the Department of Physiotherapy followed by 6 months home based programme. Bowel management including toilet training, dietary advice, medications and enemas were started before the pelvic floor muscle exercise and continued throughout the programme. Soiling frequency rank, Rintala continence score, sphincter muscle electromyography (EMG) and anorectal manometry were assessed before and after the programme. Wilcoxon signed rank test was performed for statistical analysis. From March 2001 to May 2006, 17 children were referred to the programme. Twelve patients (M:F = 10:2; age = 5-17 years) completed the programme. There was a trend of improvement in Rintala score at sixth month (p = 0.206) and at the end of programme (p = 0.061). Faecal soiling was significantly improved at sixth month (p = 0.01) and at the end of the programme (p = 0.004). Mean sphincter muscle EMG before treatment was 1.699 microV. Mean EMG at sixth month and after the programme was 3.308 microV (p = 0.034) and 3.309 microV (p = 0.002) respectively. After the programme, there was a mean increase in anal sphincter squeeze pressure of 29.9 mmHg (p = 0.007). Electrical stimulation and biofeedback exercise of pelvic floor muscle is an effective adjunct for the treatment of faecal incontinence in children following surgery for anorectal malformation.